Genomic Characterization and Surveillance of Microbial Threats in West Africa

项目摘要--总体 西非最近爆发的病毒疫情，特别是2013-16年的埃博拉病毒疫情，揭示了 关于当前监测和诊断在该区域公共卫生方面的许多局限性 系统。用于对患者样本进行快速、准确诊断和基因组分析的工具 在受疾病影响最严重的地区往往不容易获得，使其 在疫情期间更难降低发病率和死亡率。有必要让非洲人 利用广泛的基因组技术和数据更多地参与当地的研究，以便 提高患者救治水平。。该提案旨在描述和调查微生物威胁。 在整个西非，如埃博拉、拉沙热和疟疾，通过建立在长期 尼日利亚现有的学术、研究和临床中心之间的合作努力(Run， ISTH)、塞内加尔(UCAD)和塞拉利昂(KGH)，以及在美国的其他合作伙伴 布罗德学院和杜兰大学。提议的协作中心将(1)利用NEXT 世代测序和微生物元基因组学技术来鉴定和表征 研究地点传播的病毒病原体的性质和范围；(2)制定强有力的和成本低廉的- 有效的现场诊断，同时使用分子和免疫分析来快速准确地 捕获这些病原体在人群中的流行情况，以及(3)使用该基因组和 免疫学数据，以及对这些疾病的临床表现的研究，以 确定病原体-宿主相互作用的特征并加强临床护理。此外，建议的 该项目将大幅提高非洲科学家在 基因组学，通过改善项目现场的技术资源和通过密集的 在非洲和美国的地点进行基因组学和生物信息学方面的培训。具体地说，使用 Illumina MiSeq仪器目前在尼日利亚和塞内加尔现场(即将进入塞拉利昂 Leone)，我们将进一步扩展下一代测序和计算的能力 分析..这些活动服务于我们推动更多研究活动的总体战略目标 到非洲的地点，并使非洲科学家能够进行尖端基因组感染 疾病研究和发现完全在非洲大陆范围内。

Project Summary – Overall Recent viral outbreaks in West Africa, specifically the 2013-16 Ebola Virus Outbreak, shed light on the many limitations of current surveillance and diagnostics in the region's public health systems. Tools for rapid, accurate diagnostics and genomic analysis of patient samples were often not readily available in the areas that were most severely affected by the disease, making it more difficult to reduce morbidity and mortality during the epidemic. There is a need for Africans to get more engaged in locally using the wide array of genomic techniques and data in order to improve patient treatment. . This proposal aims to characterize and survey microbial threats across West Africa, such as Ebola, Lassa fever, and malaria, by building on a long-term collaborative effort among established academic, research and clinical centers in Nigeria (RUN, ISTH), Senegal (UCAD), and Sierra Leone (KGH), along with additional partners in the US at the Broad Institute and Tulane University. The proposed collaborative center will (1) utilize next generation sequencing and microbial metagenomics technologies to identify and characterize the nature and extent of circulating viral pathogens at the study sites; (2) develop robust and cost- effective field diagnostics, using both molecular and immunoassays to swiftly and accurately capture the prevalence of these pathogens in the population, and (3) use this genomic and immunological data, along with studies on the clinical manifestations of these diseases, to characterize the pathogen-host interaction and enhance clinical care. In addition the proposed project will substantially increase the building capacity for African scientists in the field of genomics, both by improving the technical resources at the project sites and through intensive training in genomics and bioinformatics at both the African and US sites. Specifically, using Illumina MiSeq instruments currently on site in Nigeria and Senegal (and coming soon to Sierra Leone), we will further expand capacity for next generation sequencing and computational analysis.. These activities serve our overall strategic goals of moving more research operations to African sites and empowering African scientists to perform cutting-edge genomic infectious disease research and discovery fully within the continent.